IQ-TREE multicore version 1.6.11 for Linux 64-bit built Jun  6 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    rabi (SSE4.2, 15 GB RAM)
Command: ../../iqtree -s Troglosironidae_28S.mafft.fasta -m TESTNEW -bb 1000 -alrt 1000
Seed:    230405 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Nov  5 23:21:51 2019
Kernel:  SSE2 - 1 threads (24 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 24 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file Troglosironidae_28S.mafft.fasta ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 36 sequences with 2063 columns, 318 distinct patterns
106 parsimony-informative, 148 singleton sites, 1809 constant sites
                               Gap/Ambiguity  Composition  p-value
   1  H_tama_IZ134691                  2.38%    passed     94.20%
   2  M_savannahensis_IZ134557         2.28%    passed     70.41%
   3  O_cameroonensis_IZ132315         4.02%    passed     73.78%
   4  P_gabonica_IZ132297              2.57%    passed     57.89%
   5  Troglosiro_sp_IZ134781          35.87%    passed     99.63%
   6  Troglosiro_sp_IZ134783          35.77%    passed     97.36%
   7  Troglosiro_sp_IZ134784          35.77%    passed     96.99%
   8  T_pseudojuberthiei_IZ133859_1   35.72%    passed     97.79%
   9  T_pseudojuberthiei_IZ133859_2   38.10%    passed     99.86%
  10  Troglosiro_sp_IZ134782          35.77%    passed     98.17%
  11  T_ninqua_IZ134768                0.05%    passed     98.96%
  12  T_wilsoni_IZ134787               2.91%    passed     95.59%
  13  T_oscitatio_IZ72572              2.76%    passed     99.57%
  14  T_longifossa_IZ65208             0.05%    passed     99.17%
  15  T_urbanus_IZ134780m              6.16%    passed     96.98%
  16  T_urbanus_IZ134780f             14.78%    passed     92.16%
  17  T_pin_IZ133854_1                 0.15%    passed     99.50%
  18  T_pseudojuberthiei_IZ151618_1   38.68%    passed     73.41%
  19  T_pseudojuberthiei_IZ151618_2   38.68%    passed     73.41%
  20  T_pseudojuberthiei_IZ133855_1    0.82%    passed     99.69%
  21  T_pseudojuberthiei_IZ133856      0.92%    passed     99.54%
  22  T_pseudojuberthiei_IZ133857_2    2.38%    passed     99.91%
  23  T_juberthiei_IZ134763f           4.07%    passed     99.31%
  24  T_cf_platnicki_IZ134766          0.44%    passed     98.38%
  25  T_juberthiei_IZ134767_1          0.44%    passed     98.38%
  26  T_brevifossa_IZ134776            9.60%    passed     90.39%
  27  T_juberthiei_IZ134763m           1.79%    passed     99.56%
  28  T_monteithi_IZ51948              8.73%    passed     99.13%
  29  T_sharmai_IZ151558_1            38.68%    passed     81.22%
  30  T_sharmai_IZ151558_2            38.73%    passed     79.38%
  31  T_dogny_IZ151570_1              38.68%    passed     79.11%
  32  T_dogny_IZ151570_2              38.68%    passed     79.11%
  33  T_sheari_IZ72565                 5.87%    passed     99.58%
  34  T_aelleni_IZ134764               0.05%    passed     99.12%
  35  T_raveni_IZ134777                3.93%    passed     99.89%
  36  T_oscitatio_IZ134779F           73.34%    passed     48.03%
WARNING: 1 sequences contain more than 50% gaps/ambiguity
****  TOTAL                           16.66%  0 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: T_pseudojuberthiei_IZ151618_2 is identical to T_pseudojuberthiei_IZ151618_1 but kept for subsequent analysis
NOTE: T_juberthiei_IZ134767_1 is identical to T_cf_platnicki_IZ134766 but kept for subsequent analysis
NOTE: T_dogny_IZ151570_2 is identical to T_dogny_IZ151570_1 but kept for subsequent analysis


Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 seconds
NOTE: ModelFinder requires 4 MB RAM!
ModelFinder will test 286 DNA models (sample size: 2063) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  JC            5179.044     69  10496.088    10500.935    10884.691
  2  JC+I          5039.739     70  10219.478    10224.468    10613.713
  3  JC+G4         5048.369     70  10236.738    10241.728    10630.972
  4  JC+I+G4       5036.947     71  10215.895    10221.030    10615.761
  5  JC+R2         5034.016     71  10210.032    10215.167    10609.898
  6  JC+R3         5033.751     73  10213.501    10218.933    10624.631
 14  F81+F         5151.017     72  10446.034    10451.316    10851.532
 15  F81+F+I       5011.418     73  10168.837    10174.268    10579.966
 16  F81+F+G4      5020.078     73  10186.156    10191.588    10597.286
 17  F81+F+I+G4    5008.794     74  10165.588    10171.171    10582.349
 18  F81+F+R2      5006.353     74  10160.707    10166.290    10577.469
 19  F81+F+R3      5006.217     76  10164.434    10170.327    10592.459
 27  K2P           5100.028     70  10340.055    10345.045    10734.289
 28  K2P+I         4955.369     71  10052.738    10057.873    10452.604
 29  K2P+G4        4965.583     71  10073.166    10078.301    10473.032
 30  K2P+I+G4      4952.235     72  10048.470    10053.752    10453.968
 31  K2P+R2        4948.237     72  10040.474    10045.756    10445.972
 32  K2P+R3        4947.989     74  10043.977    10049.561    10460.739
 40  HKY+F         5069.221     73  10284.442    10289.874    10695.572
 41  HKY+F+I       4918.799     74  9985.597     9991.181     10402.359
 42  HKY+F+G4      4930.588     74  10009.176    10014.759    10425.938
 43  HKY+F+I+G4    4916.442     75  9982.885     9988.622     10405.279
 44  HKY+F+R2      4914.583     75  9979.167     9984.904     10401.561
 45  HKY+F+R3      4914.574     77  9983.148     9989.200     10416.806
 53  TNe           5096.514     71  10335.027    10340.162    10734.893
 54  TNe+I         4954.773     72  10053.546    10058.828    10459.044
 55  TNe+G4        4964.140     72  10072.281    10077.563    10477.779
 56  TNe+I+G4      4951.241     73  10048.482    10053.914    10459.612
 57  TNe+R2        4946.678     73  10039.357    10044.788    10450.486
 58  TNe+R3        4946.413     75  10042.826    10048.563    10465.220
 66  TN+F          5061.633     74  10271.265    10276.849    10688.027
 67  TN+F+I        4917.304     75  9984.608     9990.345     10407.001
 68  TN+F+G4       4927.243     75  10004.487    10010.224    10426.881
 69  TN+F+I+G4     4914.130     76  9980.261     9986.154     10408.287
 70  TN+F+R2       4910.824     76  9973.648     9979.542     10401.674
 71  TN+F+R3       4910.651     78  9977.302     9983.513     10416.591
 79  K3P           5097.904     71  10337.808    10342.943    10737.674
 80  K3P+I         4953.006     72  10050.013    10055.295    10455.511
 81  K3P+G4        4963.237     72  10070.474    10075.756    10475.972
 82  K3P+I+G4      4949.711     73  10045.423    10050.855    10456.553
 83  K3P+R2        4946.031     73  10038.062    10043.494    10449.192
 84  K3P+R3        4945.825     75  10041.651    10047.388    10464.044
 92  K3Pu+F        5066.209     74  10280.418    10286.002    10697.180
 93  K3Pu+F+I      4914.520     75  9979.041     9984.778     10401.435
 94  K3Pu+F+G4     4926.591     75  10003.182    10008.920    10425.576
 95  K3Pu+F+I+G4   4912.212     76  9976.424     9982.318     10404.450
 96  K3Pu+F+R2     4911.120     76  9974.240     9980.134     10402.266
 97  K3Pu+F+R3     4911.098     78  9978.195     9984.407     10417.485
105  TPM2+F        5061.913     74  10271.826    10277.409    10688.588
106  TPM2+F+I      4904.159     75  9958.319     9964.056     10380.713
107  TPM2+F+G4     4917.700     75  9985.400     9991.137     10407.794
108  TPM2+F+I+G4   4902.152     76  9956.304     9962.197     10384.330
109  TPM2+F+R2     4902.006     76  9956.013     9961.906     10384.038
110  TPM2+F+R3     4901.947     78  9959.893     9966.105     10399.183
118  TPM2u+F       5061.948     74  10271.897    10277.480    10688.659
119  TPM2u+F+I     4904.192     75  9958.385     9964.122     10380.778
120  TPM2u+F+G4    4917.730     75  9985.461     9991.198     10407.855
121  TPM2u+F+I+G4  4902.167     76  9956.333     9962.226     10384.359
122  TPM2u+F+R2    4901.908     76  9955.816     9961.709     10383.841
123  TPM2u+F+R3    4901.828     78  9959.655     9965.867     10398.945
131  TPM3+F        5055.950     74  10259.900    10265.484    10676.662
132  TPM3+F+I      4905.383     75  9960.766     9966.503     10383.160
133  TPM3+F+G4     4916.341     75  9982.682     9988.420     10405.076
134  TPM3+F+I+G4   4902.265     76  9956.530     9962.423     10384.556
135  TPM3+F+R2     4900.421     76  9952.843     9958.736     10380.868
136  TPM3+F+R3     4900.305     78  9956.611     9962.822     10395.900
144  TPM3u+F       5055.950     74  10259.900    10265.483    10676.662
145  TPM3u+F+I     4905.385     75  9960.770     9966.507     10383.164
146  TPM3u+F+G4    4916.341     75  9982.683     9988.420     10405.076
147  TPM3u+F+I+G4  4902.227     76  9956.453     9962.346     10384.479
148  TPM3u+F+R2    4900.422     76  9952.845     9958.738     10380.870
149  TPM3u+F+R3    4900.305     78  9956.611     9962.823     10395.900
157  TIMe          5094.374     72  10332.749    10338.031    10738.247
158  TIMe+I        4952.389     73  10050.779    10056.210    10461.908
159  TIMe+G4       4961.775     73  10069.550    10074.981    10480.679
160  TIMe+I+G4     4948.568     74  10045.137    10050.720    10461.899
161  TIMe+R2       4944.676     74  10037.352    10042.936    10454.114
162  TIMe+R3       4944.357     76  10040.713    10046.606    10468.739
170  TIM+F         5058.595     75  10267.191    10272.928    10689.585
171  TIM+F+I       4913.053     76  9978.107     9984.000     10406.133
172  TIM+F+G4      4923.257     76  9998.515     10004.408    10426.540
173  TIM+F+I+G4    4909.812     77  9973.624     9979.675     10407.282
174  TIM+F+R2      4907.405     77  9968.810     9974.862     10402.468
175  TIM+F+R3      4907.240     79  9972.480     9978.854     10417.401
183  TIM2e         5092.834     72  10329.668    10334.950    10735.166
184  TIM2e+I       4947.577     73  10041.154    10046.586    10452.284
185  TIM2e+G4      4958.063     73  10062.126    10067.557    10473.255
186  TIM2e+I+G4    4943.996     74  10035.992    10041.576    10452.754
187  TIM2e+R2      4940.731     74  10029.462    10035.045    10446.224
188  TIM2e+R3      4940.518     76  10033.036    10038.929    10461.062
196  TIM2+F        5054.381     75  10258.761    10264.498    10681.155
197  TIM2+F+I      4903.174     76  9958.348     9964.241     10386.373
198  TIM2+F+G4     4914.927     76  9981.854     9987.747     10409.879
199  TIM2+F+I+G4   4900.135     77  9954.270     9960.321     10387.928
200  TIM2+F+R2     4898.491     77  9950.982     9957.033     10384.640
201  TIM2+F+R3     4898.484     79  9954.968     9961.342     10399.889
209  TIM3e         5087.905     72  10319.809    10325.092    10725.307
210  TIM3e+I       4946.278     73  10038.556    10043.988    10449.686
211  TIM3e+G4      4955.490     73  10056.980    10062.412    10468.110
212  TIM3e+I+G4    4942.183     74  10032.367    10037.950    10449.129
213  TIM3e+R2      4938.548     74  10025.096    10030.680    10441.858
214  TIM3e+R3      4938.301     76  10028.602    10034.495    10456.627
222  TIM3+F        5048.297     75  10246.594    10252.331    10668.987
223  TIM3+F+I      4903.855     76  9959.710     9965.604     10387.736
224  TIM3+F+G4     4912.911     76  9977.821     9983.715     10405.847
225  TIM3+F+I+G4   4899.535     77  9953.071     9959.122     10386.728
226  TIM3+F+R2     4896.996     77  9947.991     9954.042     10381.649
227  TIM3+F+R3     4896.869     79  9951.737     9958.111     10396.659
235  TVMe          5084.912     73  10315.824    10321.256    10726.954
236  TVMe+I        4936.210     74  10020.420    10026.004    10437.182
237  TVMe+G4       4947.615     74  10043.229    10048.813    10459.991
238  TVMe+I+G4     4932.903     75  10015.805    10021.542    10438.199
239  TVMe+R2       4931.059     75  10012.119    10017.856    10434.513
240  TVMe+R3       4930.974     77  10015.948    10021.999    10449.605
248  TVM+F         5045.794     76  10243.587    10249.480    10671.613
249  TVM+F+I       4887.552     77  9929.104     9935.155     10362.762
250  TVM+F+G4      4900.357     77  9954.714     9960.766     10388.372
251  TVM+F+I+G4    4884.555     78  9925.110     9931.322     10364.400
252  TVM+F+R2      4884.470     78  9924.941     9931.152     10364.230
253  TVM+F+R3      4884.365     80  9928.730     9935.269     10379.283
261  SYM           5081.436     74  10310.872    10316.456    10727.634
262  SYM+I         4935.802     75  10021.604    10027.341    10443.997
263  SYM+G4        4946.309     75  10042.617    10048.355    10465.011
264  SYM+I+G4      4932.034     76  10016.068    10021.961    10444.094
265  SYM+R2        4929.655     76  10011.311    10017.204    10439.336
266  SYM+R3        4929.481     78  10014.963    10021.175    10454.252
274  GTR+F         5038.251     77  10230.502    10236.554    10664.160
275  GTR+F+I       4886.586     78  9929.173     9935.385     10368.462
276  GTR+F+G4      4897.513     78  9951.026     9957.238     10390.315
277  GTR+F+I+G4    4882.519     79  9923.039     9929.413     10367.960
278  GTR+F+R2      4881.083     79  9920.165     9926.539     10365.086
279  GTR+F+R3      4881.016     81  9924.032     9930.738     10380.217
Akaike Information Criterion:           GTR+F+R2
Corrected Akaike Information Criterion: GTR+F+R2
Bayesian Information Criterion:         TVM+F+I
Best-fit model: TVM+F+I chosen according to BIC

All model information printed to Troglosironidae_28S.mafft.fasta.model.gz
CPU time for ModelFinder: 6.806 seconds (0h:0m:6s)
Wall-clock time for ModelFinder: 6.958 seconds (0h:0m:6s)
Generating 1000 samples for ultrafast bootstrap (seed: 230405)...

NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -5100.916
2. Current log-likelihood: -4908.905
3. Current log-likelihood: -4887.658
4. Current log-likelihood: -4887.554
Optimal log-likelihood: -4887.551
Rate parameters:  A-C: 1.15135  A-G: 4.17462  A-T: 2.24758  C-G: 0.05879  C-T: 4.17462  G-T: 1.00000
Base frequencies:  A: 0.217  C: 0.262  G: 0.329  T: 0.193
Proportion of invariable sites: 0.826
Parameters optimization took 4 rounds (0.078 sec)
Computing ML distances based on estimated model parameters... 0.006 sec
Computing BIONJ tree...
0.028 seconds
Log-likelihood of BIONJ tree: -4952.075
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.236 second
Computing log-likelihood of 98 initial trees ... 0.433 seconds
Current best score: -4880.049

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -4877.928
Iteration 10 / LogL: -4881.844 / Time: 0h:0m:1s
Iteration 20 / LogL: -4881.613 / Time: 0h:0m:2s
Finish initializing candidate tree set (20)
Current best tree score: -4877.928 / CPU time: 2.170
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
BETTER TREE FOUND at iteration 24: -4877.926
UPDATE BEST LOG-LIKELIHOOD: -4877.926
Iteration 30 / LogL: -4882.512 / Time: 0h:0m:3s (0h:0m:11s left)
UPDATE BEST LOG-LIKELIHOOD: -4877.924
UPDATE BEST LOG-LIKELIHOOD: -4877.924
Iteration 40 / LogL: -4878.447 / Time: 0h:0m:4s (0h:0m:9s left)
Iteration 50 / LogL: -4879.042 / Time: 0h:0m:4s (0h:0m:7s left)
Log-likelihood cutoff on original alignment: -4899.518
Iteration 60 / LogL: -4881.086 / Time: 0h:0m:5s (0h:0m:6s left)
Iteration 70 / LogL: -4877.925 / Time: 0h:0m:6s (0h:0m:5s left)
BETTER TREE FOUND at iteration 77: -4877.921
Iteration 80 / LogL: -4877.923 / Time: 0h:0m:7s (0h:0m:9s left)
Iteration 90 / LogL: -4877.922 / Time: 0h:0m:8s (0h:0m:7s left)
Iteration 100 / LogL: -4920.901 / Time: 0h:0m:8s (0h:0m:6s left)
Log-likelihood cutoff on original alignment: -4900.116
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.997
BETTER TREE FOUND at iteration 107: -4877.921
Iteration 110 / LogL: -4931.649 / Time: 0h:0m:9s (0h:0m:8s left)
Iteration 120 / LogL: -4881.715 / Time: 0h:0m:10s (0h:0m:7s left)
UPDATE BEST LOG-LIKELIHOOD: -4877.919
Iteration 130 / LogL: -4877.921 / Time: 0h:0m:11s (0h:0m:6s left)
UPDATE BEST LOG-LIKELIHOOD: -4877.918
Iteration 140 / LogL: -4877.920 / Time: 0h:0m:12s (0h:0m:5s left)
Iteration 150 / LogL: -4881.391 / Time: 0h:0m:12s (0h:0m:4s left)
Log-likelihood cutoff on original alignment: -4900.116
UPDATE BEST LOG-LIKELIHOOD: -4877.917
Iteration 160 / LogL: -4877.920 / Time: 0h:0m:13s (0h:0m:4s left)
UPDATE BEST LOG-LIKELIHOOD: -4877.913
Iteration 170 / LogL: -4877.919 / Time: 0h:0m:14s (0h:0m:3s left)
Iteration 180 / LogL: -4877.914 / Time: 0h:0m:15s (0h:0m:2s left)
Iteration 190 / LogL: -4881.011 / Time: 0h:0m:16s (0h:0m:1s left)
Iteration 200 / LogL: -4877.916 / Time: 0h:0m:16s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4900.116
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.995
TREE SEARCH COMPLETED AFTER 208 ITERATIONS / Time: 0h:0m:17s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -4877.913
Optimal log-likelihood: -4877.904
Rate parameters:  A-C: 1.12762  A-G: 4.08286  A-T: 2.11097  C-G: 0.05664  C-T: 4.08286  G-T: 1.00000
Base frequencies:  A: 0.217  C: 0.262  G: 0.329  T: 0.193
Proportion of invariable sites: 0.826
Parameters optimization took 1 rounds (0.012 sec)
BEST SCORE FOUND : -4877.904

Testing tree branches by SH-like aLRT with 1000 replicates...
1.205 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file Troglosironidae_28S.mafft.fasta.splits.nex
Total tree length: 0.266

Total number of iterations: 208
CPU time used for tree search: 16.644 sec (0h:0m:16s)
Wall-clock time used for tree search: 17.359 sec (0h:0m:17s)
Total CPU time used: 18.111 sec (0h:0m:18s)
Total wall-clock time used: 19.015 sec (0h:0m:19s)

Computing bootstrap consensus tree...
Reading input file Troglosironidae_28S.mafft.fasta.splits.nex...
36 taxa and 483 splits.
Consensus tree written to Troglosironidae_28S.mafft.fasta.contree
Reading input trees file Troglosironidae_28S.mafft.fasta.contree
Log-likelihood of consensus tree: -4877.920

Analysis results written to: 
  IQ-TREE report:                Troglosironidae_28S.mafft.fasta.iqtree
  Maximum-likelihood tree:       Troglosironidae_28S.mafft.fasta.treefile
  Likelihood distances:          Troglosironidae_28S.mafft.fasta.mldist

Ultrafast bootstrap approximation results written to:
  Split support values:          Troglosironidae_28S.mafft.fasta.splits.nex
  Consensus tree:                Troglosironidae_28S.mafft.fasta.contree
  Screen log file:               Troglosironidae_28S.mafft.fasta.log

Date and Time: Tue Nov  5 23:22:17 2019
